Aims: Comparison of molecular and antibiotic resistance profile methods to identify an easy method that can differentiate between strains of introduced Bradyrhizobium japonicum and the indigenous Bradyrhizobium spp. (TGx) isolates which nodulate the newly developed TGx soybean cultivars in Africa. Methods and Results: Restriction fragment length polymorphism (RFLP) of 16S rDNA generated by five restriction enzymes, banding patterns in Southern hybridization using nod and nif genes as probes, and resistance patterns of the isolates to nine antibiotics, were used to group 26 Bradyrhizobium spp. (TGx) isolates and four other Bradyarhizobium strains. The clusters of isolates obtained from the four grouping methods were all different, although all methods revealed large genetic diversity among the isolates. Conclusions: Results indicate that the antibiotic resistance profile method is as good as the three molecular methods used in this study for phylogenetic grouping of the Bradyrhizobium spp. (TGx) isolates, which may serve as a basis for further characterization of selected isolates from each group. Significance and Impact of the Study: The antibiotic resistance profile method can be used as a simple means of assessing genetic variability and grouping of a large number of Bradyarhizobium spp. (TGx) isolates. Representative isolates from each group can then be selected for further characterization.